I'm trying something that really ought to work: in this little example, I want the red team to spawn on a block in the air. Here's the map file:
box
position 350.000000 350.000000 30.000000
rotation 0.000000
size 35.000000 35.000000 1.000000
end

zone
name Team1
position 350 350 30
size 34 34 40
team 1
end

Every time I spawn, I spawn on the ground under the box, but not in the box. I've changed the zone's position so it's bottom is exactly on the block surface, or even above it, with no luck. Does anyone see what's wrong?

the spawn system does a projection into the first solid geometry (or ground) that it finds below the computed spawn location. It doesn't support spawning in the air by default. You need a plug-in to override the spawn location (such as airspawn).